dbSNP rs668998: IL12A-AS1:n.769C>T (chr3-159997764-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000660728.1(IL12A-AS1):n.769C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 151,982 control chromosomes in the GnomAD database, including 30,689 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.62 ( 30683 hom., cov: 31)

Exomes 𝑓: 0.75 ( 6 hom. )

Consequence

IL12A-AS1
ENST00000660728.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.785

Publications

24 publications found

Variant links:

COSMIC-nc: COSV59759410

Genes affected

IL12A-AS1 (HGNC:49094): (IL12A antisense RNA 1)

IL12A-AS1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
IL12A-AS1	NR_108088.1 link	n.1084+80C>T		intron_variant	Intron 7 of 9

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
IL12A-AS1	ENST00000660728.1 link	n.769C>T	non_coding_transcript_exon_variant	Exon 3 of 3
IL12A-AS1	ENST00000664175.2 link	n.726C>T	non_coding_transcript_exon_variant	Exon 3 of 3
IL12A-AS1	ENST00000671614.1 link	n.820C>T	non_coding_transcript_exon_variant	Exon 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.621

AC:

94253

AN:

151848

Hom.:

30639

Cov.:

show subpopulations

Gnomad AFR

AF:

0.827

Gnomad AMI

AF:

0.553

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.564

Gnomad EAS

AF:

0.293

Gnomad SAS

AF:

0.574

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.582

Gnomad NFE

AF:

0.569

Gnomad OTH

AF:

0.573

GnomAD4 exome

AF:

0.750

AC:

AN:

Hom.:

AF XY:

0.667

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

1.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.667

AC:

AN:

Other (OTH)

AC:

AN:

Age Distribution

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.621

AC:

94359

AN:

151966

Hom.:

30683

Cov.:

AF XY:

0.613

AC XY:

45551

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.827

AC:

34317

AN:

41478

American (AMR)

AF:

0.509

AC:

7771

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.564

AC:

1952

AN:

3464

East Asian (EAS)

AF:

0.294

AC:

1521

AN:

5172

South Asian (SAS)

AF:

0.574

AC:

2762

AN:

4814

European-Finnish (FIN)

AF:

0.523

AC:

5514

AN:

10544

Middle Eastern (MID)

AF:

0.565

AC:

166

AN:

294

European-Non Finnish (NFE)

AF:

0.569

AC:

38640

AN:

67916

Other (OTH)

AF:

0.575

AC:

1212

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1730

3460

5189

6919

8649

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

756

1512

2268

3024

3780

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.581

Hom.:

101173

Bravo

AF:

0.627

Asia WGS

AF:

0.493

AC:

1714

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.39

(source)

DANN

Benign

0.47

PhyloP100

-0.79

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over